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PMC:7443692 / 32781-35203 JSONTXT

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LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T191 460-467 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T192 566-573 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T193 732-739 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T194 1393-1400 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T195 1958-1965 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T196 2007-2014 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T197 2050-2057 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T198 2241-2248 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T199 2346-2353 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T91 398-408 Species denotes SARS-CoV-2 NCBItxid:2697049
T92 1674-1679 Species denotes Human NCBItxid:9606
T93 1702-1712 Species denotes SARS-CoV-2 NCBItxid:2697049
T94 1828-1833 Species denotes human NCBItxid:9606
T95 1856-1866 Species denotes SARS-CoV-2 NCBItxid:2697049
T96 2382-2387 Species denotes human NCBItxid:9606

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T199 0-124 Sentence denotes MD simulations were performed to examine the co-complex (generated from a crystal structure of the ACE2-RBD co-complex, PDB:
T200 125-307 Sentence denotes 6M0J; Lan et al., 2020) of glycosylated S with glycosylated ACE2 with the three different glycoforms models (Abundance, Oxford Class, and Processed; Table S1; Videos S5, S6, and S7).
T201 308-546 Sentence denotes Information from these analyses is laid out along the primary structure (sequence) of the SARS-CoV-2 S protomer and ACE2 highlighting regions of glycan-protein interaction observed in the MD simulations (Table S14; Videos S5, S6, and S7).
T202 547-752 Sentence denotes Interestingly, two glycans on ACE2 (at N090 and N322), which are highlighted in Figure 7 A and shown in a more close-up view in Figure 7B, are predicted to form interactions with the S protein (Table S15).
T203 753-975 Sentence denotes The N322 glycan interaction with the S trimer is outside of the receptor-binding domain, and the interaction is observed across multiple simulations and throughout each simulation (Figures 7A and 7B; Video S5, S6, and S7).
T204 976-1267 Sentence denotes The ACE2 glycan at N090 is close enough to the S trimer surface to repeatedly form interactions; however, the glycan arms interact with multiple regions of the surface over the course of the simulations, reflecting the relatively high degree of glycan dynamics (Figures 7A and 7B; Video S3).
T205 1268-1452 Sentence denotes Inter-molecule glycan-glycan interactions are also observed repeatedly between the glycan at N546 of ACE2 and those in the S protein at residues N0074 and N0165 (Figure 7D; Table S16).
T206 1453-1627 Sentence denotes Finally, a full view of the ACE2-S complex with Oxford class glycoforms on ACE2 illustrates the extensive glycosylation at the interface of the complex (Figure 7C; Video S4).
T207 1628-1785 Sentence denotes Figure 7 Interactions of Glycosylated Soluble Human ACE2 and Glycosylated SARS-CoV-2 S Trimer Immunogen Revealed By 3D-Structural Modeling and MD Simulations
T208 1786-1926 Sentence denotes (A) MD simulation of glycosylated soluble human ACE2 and glycosylated SARS-CoV-2 S trimer immunogen interaction (see Videos S5, S6, and S7).
T209 1927-2028 Sentence denotes ACE2 (top) is colored red with glycans in pink, whereas S is colored white with glycans in dark gray.
T210 2029-2111 Sentence denotes Highlighted are ACE2 glycans that interact with S that are magnified to the right.
T211 2112-2301 Sentence denotes (B) Magnification of ACE2-S interface highlighting ACE2 glycan interactions by using 3D-SNFG icons (Thieker et al., 2016) with S protein (pink) as well as ACE2-S glycan-glycan interactions.
T212 2302-2422 Sentence denotes (C) Magnification of dynamics trajectory of glycans at the interface of soluble human ACE2 and S (see Videos S3 and S4).

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T61 398-408 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T62 1702-1712 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T63 1856-1866 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T2169 99-103 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2170 104-107 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T2179 185-189 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2180 424-428 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2181 518-521 Protein denotes S14 https://www.uniprot.org/uniprot/Q92748|https://www.uniprot.org/uniprot/Q63536|https://www.uniprot.org/uniprot/Q62264|https://www.uniprot.org/uniprot/P04143|https://www.uniprot.org/uniprot/B2R4W7
T2186 577-581 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2187 730-739 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T2220 980-984 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2221 1369-1373 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2222 1391-1400 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T2255 1464-1468 Protein denotes full https://www.uniprot.org/uniprot/Q8N1N2
T2256 1481-1485 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2257 1528-1532 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2258 1680-1684 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2259 1834-1838 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2260 1927-1931 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2261 2045-2049 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2262 2133-2137 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2263 2163-2167 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2264 2239-2248 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T2297 2267-2271 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T2298 2388-2392 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T100 460-467 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T101 732-739 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T102 1393-1400 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T103 2241-2248 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T76 1559-1572 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T72 1559-1572 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

2_test

Id Subject Object Predicate Lexical cue
32841605-32225176-19659521 143-147 32225176 denotes 2020
32841605-27514939-19659522 2228-2232 27514939 denotes 2016